1.810 Å
X-ray
2012-04-12
Name: | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component |
---|---|
ID: | TODA_PSEP1 |
AC: | A5W4E9 |
Organism: | Pseudomonas putida |
Reign: | Bacteria |
TaxID: | 351746 |
EC Number: | 1.18.1.3 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 24.705 |
---|---|
Number of residues: | 53 |
Including | |
Standard Amino Acids: | 47 |
Non Standard Amino Acids: | 1 |
Water Molecules: | 5 |
Cofactors: | FAD |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.762 | 725.625 |
% Hydrophobic | % Polar |
---|---|
46.98 | 53.02 |
According to VolSite |
HET Code: | NAD |
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Formula: | C21H26N7O14P2 |
Molecular weight: | 662.417 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 65.19 % |
Polar Surface area: | 343.54 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 18 |
H-Bond Donors: | 6 |
Rings: | 5 |
Aromatic rings: | 3 |
Anionic atoms: | 2 |
Cationic atoms: | 1 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 11 |
X | Y | Z |
---|---|---|
-3.6617 | 25.4344 | 14.861 |
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
Ligand | Protein | Interaction | |||
---|---|---|---|---|---|
Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
N7A | NH2 | ARG- 112 | 3.23 | 128.53 | H-Bond (Protein Donor) |
O2A | N | LEU- 153 | 3.26 | 176.48 | H-Bond (Protein Donor) |
C2D | CD1 | LEU- 153 | 4.37 | 0 | Hydrophobic |
C4N | CB | LEU- 153 | 3.78 | 0 | Hydrophobic |
O1N | N | ILE- 154 | 2.92 | 149.36 | H-Bond (Protein Donor) |
C5D | CD1 | ILE- 154 | 3.81 | 0 | Hydrophobic |
C5N | CG1 | ILE- 154 | 3.69 | 0 | Hydrophobic |
N7N | OE2 | GLU- 157 | 3.15 | 161.89 | H-Bond (Ligand Donor) |
O3B | OE1 | GLU- 173 | 2.6 | 153.02 | H-Bond (Ligand Donor) |
O2B | OE2 | GLU- 173 | 2.55 | 158.79 | H-Bond (Ligand Donor) |
N3A | N | ALA- 174 | 3.32 | 150.77 | H-Bond (Protein Donor) |
O1A | NE | ARG- 181 | 3.02 | 145.38 | H-Bond (Protein Donor) |
O2A | NH1 | ARG- 181 | 3.01 | 167.73 | H-Bond (Protein Donor) |
O2D | NH1 | ARG- 181 | 2.91 | 145.24 | H-Bond (Protein Donor) |
O1A | CZ | ARG- 181 | 3.7 | 0 | Ionic (Protein Cationic) |
O2A | CZ | ARG- 181 | 3.87 | 0 | Ionic (Protein Cationic) |
O2N | N | GLY- 238 | 3.09 | 136.01 | H-Bond (Protein Donor) |
C4D | CB | ALA- 239 | 3.82 | 0 | Hydrophobic |
O3D | OE1 | GLU- 290 | 2.64 | 158.63 | H-Bond (Ligand Donor) |
O2D | O | GLU- 290 | 3.21 | 139.32 | H-Bond (Ligand Donor) |
N7N | O | TRP- 320 | 2.7 | 164.04 | H-Bond (Ligand Donor) |
C5N | C7M | FAD- 501 | 4.31 | 0 | Hydrophobic |
O1N | O | HOH- 640 | 2.61 | 179.99 | H-Bond (Protein Donor) |
O1A | O | HOH- 779 | 2.77 | 154.56 | H-Bond (Protein Donor) |
O3B | O | HOH- 806 | 2.97 | 145.68 | H-Bond (Protein Donor) |
O3D | O | HOH- 820 | 2.91 | 139.28 | H-Bond (Protein Donor) |